
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()

os.chdir(data_dir.name)


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
    from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
    from jwst.extract_2d.extract_2d_step import Extract2dStep
    from jwst.srctype.srctype_step import SourceTypeStep
    from jwst.wavecorr.wavecorr_step import WavecorrStep
    from jwst.flatfield.flat_field_step import FlatFieldStep
    from jwst.pathloss.pathloss_step import PathLossStep
    from jwst import datamodels

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Make sure that the version used is the right one

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.8.2
Using NPTT version:  2.0.1


testing_data = {
                
                'mos_g140m_f100lp':{
                                  'uncal_file_nrs1': 'mos_g140m_line1_NRS1_uncal.fits',
                                  'uncal_file_nrs2': 'mos_g140m_line1_NRS2_uncal.fits',  
                                  'msa_shutter_config': 'V8460001000101_msa.fits' }
               }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# Set common NPTT switches for this test

# accepted threshold difference with respect to benchmark files
threshold_diff = 9.999e-05

# other NPTT variables
writefile = False
show_figs = True
save_figs = False

# Get the data
detectors = ['nrs1', 'nrs2']
results_dict = {}
for mode_config, data_set_dict in testing_data.items():
    for det in detectors:
        print('Testing files for detector: ', det)
        data = get_artifactory_file(data_set_dict, det)
        uncal_file, msa_shutter_config = data
        print('Working with uncal_file: ', uncal_file)
        uncal_basename = os.path.basename(uncal_file)
        
        # Run the stage 1 pipeline 
        rate_object = Detector1Pipeline.call(uncal_file)
        # Make sure the MSA shutter configuration file is set up correctly
        rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
        if msa_shutter_config is not None:
            rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
            print('MSA shutter configuration file: ', rate_object.meta.instrument.msa_metadata_file)

        # Run the stage 2 pipeline steps
        try:
            pipe_object = AssignWcsStep.call(rate_object)
            skip_file = False
        except:
            print('An error occurred that made the pipeline crash, probably: No open slits fall on detector ', det)
            print("Skipping test for this file. \n")
            skip_file = True
            
        if not skip_file:                        
            if 'ifu' in uncal_basename.lower() or 'mos' in uncal_basename.lower():
                pipe_object = MSAFlagOpenStep.call(pipe_object)
            if 'ifu' not in uncal_basename.lower():
                pipe_object = Extract2dStep.call(pipe_object)
            pipe_object = SourceTypeStep.call(pipe_object)
            pipe_object = WavecorrStep.call(pipe_object)
            flat_field_object = FlatFieldStep.call(pipe_object)
            pathloss_object = PathLossStep.call(flat_field_object)

            # get the corresponding reference file from the pathloss datamodel
            reffile_path = pathloss_object.meta.ref_file.pathloss.name.replace("crds://", 
                                                    "https://jwst-crds.stsci.edu/unchecked_get/references/jwst/")

            # Run the validation test
            %matplotlib inline

            if 'mos' in uncal_file.lower():
                print('Running test for MOS...')
                median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
                                                                                     flat_field_object, 
                                                                                     reffile_path,
                                                                                     pathloss_object,
                                                                                     writefile=writefile,
                                                                                     show_figs=show_figs,
                                                                                     save_figs=save_figs,
                                                                                     threshold_diff=threshold_diff)

        else:
            result_msg = 'skipped'

        # Did the test passed 
        print("Did pathloss validation test passed? ", result_msg, "\n\n")
        rd = {uncal_basename: result_msg}
        results_dict.update(rd)
        
        # close all open files
        psutil.Process().open_files()
        closing_files = []
        for fd in psutil.Process().open_files():
            if data_dir.name in fd.path:
                closing_files.append(fd)
        for fd in closing_files:
            try:
                print('Closing file: ', fd)
                open(fd.fd).close()
            except:
                print('File already closed: ', fd)

Testing files for detector:  nrs1
Working with uncal_file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2/mos_g140m_line1_NRS1_uncal.fits

2022-12-04 02:36:44,784 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-12-04 02:36:44,824 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-12-04 02:36:44,826 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-12-04 02:36:44,827 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-12-04 02:36:44,828 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-12-04 02:36:44,829 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-12-04 02:36:44,830 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-12-04 02:36:44,831 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-12-04 02:36:44,832 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-12-04 02:36:44,833 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-12-04 02:36:44,834 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-12-04 02:36:44,835 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-12-04 02:36:44,836 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-12-04 02:36:44,837 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-12-04 02:36:44,838 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-12-04 02:36:44,839 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-12-04 02:36:44,840 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-12-04 02:36:44,842 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-12-04 02:36:44,991 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2/mos_g140m_line1_NRS1_uncal.fits',).
2022-12-04 02:36:45,003 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-12-04 02:36:45,192 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-12-04 02:36:45,200 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2022-12-04 02:36:45,201 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2022-12-04 02:36:45,203 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits'.
2022-12-04 02:36:45,204 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2022-12-04 02:36:45,206 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-12-04 02:36:45,206 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2022-12-04 02:36:45,208 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2022-12-04 02:36:45,208 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-12-04 02:36:45,209 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-12-04 02:36:45,209 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits'.
2022-12-04 02:36:45,211 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2022-12-04 02:36:45,212 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-12-04 02:36:45,213 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-12-04 02:36:45,213 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-12-04 02:36:45,585 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:45,587 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:36:45,722 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-12-04 02:36:45,723 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-12-04 02:36:45,725 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-12-04 02:36:45,845 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:45,846 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:36:45,870 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2022-12-04 02:36:46,693 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-12-04 02:36:46,812 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:46,813 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2', 'n_pix_grow_sat': 1}
2022-12-04 02:36:46,837 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits
2022-12-04 02:36:49,031 - stpipe.Detector1Pipeline.saturation - INFO - Detected 108240 saturated pixels
2022-12-04 02:36:49,058 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-12-04 02:36:49,073 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-12-04 02:36:49,206 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:49,207 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:36:49,208 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-12-04 02:36:49,210 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-12-04 02:36:49,330 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:49,331 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:36:49,356 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2022-12-04 02:36:51,638 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-12-04 02:36:51,779 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:51,780 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-12-04 02:36:51,898 - stpipe.Detector1Pipeline.refpix - INFO - NIR full frame data
2022-12-04 02:36:51,899 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are valid for this mode:
2022-12-04 02:36:51,899 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2022-12-04 02:36:51,899 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2022-12-04 02:36:51,900 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2022-12-04 02:36:51,900 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2022-12-04 02:36:51,900 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is not applicable and is ignored:
2022-12-04 02:36:51,901 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2022-12-04 02:36:54,346 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-12-04 02:36:54,490 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:54,492 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:36:54,518 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits
2022-12-04 02:36:59,497 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-12-04 02:36:59,635 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:36:59,636 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2', 'dark_output': None}
2022-12-04 02:36:59,673 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2022-12-04 02:37:04,248 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2022-12-04 02:37:04,249 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2022-12-04 02:37:04,540 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-12-04 02:37:04,655 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:04,657 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}
2022-12-04 02:37:04,667 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-12-04 02:37:04,682 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-04 02:37:04,867 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-04 02:37:05,921 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-12-04 02:37:05,979 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-12-04 02:37:08,301 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 41569 pixels with at least one CR from five or more groups.
2022-12-04 02:37:15,406 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 9.48297 sec
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:302: RuntimeWarning: invalid value encountered in divide
  data /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:303: RuntimeWarning: invalid value encountered in divide
  err /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:304: RuntimeWarning: invalid value encountered in divide
  readnoise_2d /= gain_2d
2022-12-04 02:37:15,487 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.819534
2022-12-04 02:37:15,493 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-12-04 02:37:15,630 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:15,632 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-12-04 02:37:15,669 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-04 02:37:15,670 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-04 02:37:15,785 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-12-04 02:37:15,786 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-12-04 02:37:41,792 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2022-12-04 02:37:41,793 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-12-04 02:37:41,976 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-12-04 02:37:42,129 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:42,130 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:37:42,208 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-04 02:37:42,209 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-04 02:37:42,213 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-04 02:37:42,329 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:42,330 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2'}
2022-12-04 02:37:42,405 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-04 02:37:42,406 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-04 02:37:42,411 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-04 02:37:42,411 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-12-04 02:37:42,412 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:37:42,412 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-12-04 02:37:42,423 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-04 02:37:42,540 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:42,541 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}

MSA shutter configuration file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2/V8460001000101_msa.fits

2022-12-04 02:37:42,714 - stpipe.AssignWcsStep - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2022-12-04 02:37:42,941 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-04 02:37:42,942 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-04 02:37:42,943 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-04 02:37:42,944 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-04 02:37:43,217 - stpipe.AssignWcsStep - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,230 - stpipe.AssignWcsStep - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,243 - stpipe.AssignWcsStep - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,256 - stpipe.AssignWcsStep - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,269 - stpipe.AssignWcsStep - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,283 - stpipe.AssignWcsStep - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,296 - stpipe.AssignWcsStep - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,309 - stpipe.AssignWcsStep - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,322 - stpipe.AssignWcsStep - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,336 - stpipe.AssignWcsStep - INFO - Removing slit 17 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,349 - stpipe.AssignWcsStep - INFO - Removing slit 18 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,362 - stpipe.AssignWcsStep - INFO - Removing slit 19 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,375 - stpipe.AssignWcsStep - INFO - Removing slit 21 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,389 - stpipe.AssignWcsStep - INFO - Removing slit 25 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,402 - stpipe.AssignWcsStep - INFO - Removing slit 26 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,415 - stpipe.AssignWcsStep - INFO - Removing slit 27 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,428 - stpipe.AssignWcsStep - INFO - Removing slit 29 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,441 - stpipe.AssignWcsStep - INFO - Removing slit 31 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,454 - stpipe.AssignWcsStep - INFO - Removing slit 32 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,467 - stpipe.AssignWcsStep - INFO - Removing slit 33 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,481 - stpipe.AssignWcsStep - INFO - Removing slit 35 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,496 - stpipe.AssignWcsStep - INFO - Removing slit 37 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,510 - stpipe.AssignWcsStep - INFO - Removing slit 38 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,523 - stpipe.AssignWcsStep - INFO - Removing slit 39 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,537 - stpipe.AssignWcsStep - INFO - Removing slit 41 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,577 - stpipe.AssignWcsStep - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,590 - stpipe.AssignWcsStep - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,604 - stpipe.AssignWcsStep - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,617 - stpipe.AssignWcsStep - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,631 - stpipe.AssignWcsStep - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,644 - stpipe.AssignWcsStep - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,658 - stpipe.AssignWcsStep - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,671 - stpipe.AssignWcsStep - INFO - Removing slit 20 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,684 - stpipe.AssignWcsStep - INFO - Removing slit 22 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,698 - stpipe.AssignWcsStep - INFO - Removing slit 23 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,711 - stpipe.AssignWcsStep - INFO - Removing slit 24 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,724 - stpipe.AssignWcsStep - INFO - Removing slit 28 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,736 - stpipe.AssignWcsStep - INFO - Removing slit 30 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,749 - stpipe.AssignWcsStep - INFO - Removing slit 34 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,763 - stpipe.AssignWcsStep - INFO - Removing slit 36 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:43,776 - stpipe.AssignWcsStep - INFO - Removing slit 40 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-04 02:37:44,082 - stpipe.AssignWcsStep - INFO - Slits projected on detector NRS1: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]
2022-12-04 02:37:44,083 - stpipe.AssignWcsStep - INFO - Computing WCS for 27 open slitlets
2022-12-04 02:37:44,122 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-04 02:37:44,123 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-04 02:37:44,123 - stpipe.AssignWcsStep - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-04 02:37:44,125 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-04 02:37:44,147 - stpipe.AssignWcsStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2022-12-04 02:37:44,313 - stpipe.AssignWcsStep - INFO - There are 2 open slits in quadrant 1
2022-12-04 02:37:44,331 - stpipe.AssignWcsStep - INFO - There are 11 open slits in quadrant 2
2022-12-04 02:37:44,421 - stpipe.AssignWcsStep - INFO - There are 4 open slits in quadrant 3
2022-12-04 02:37:44,452 - stpipe.AssignWcsStep - INFO - There are 10 open slits in quadrant 4
2022-12-04 02:37:44,676 - stpipe.AssignWcsStep - INFO - There are 0 open slits in quadrant 5
2022-12-04 02:37:44,860 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmplm2i7xd2/V8460001000101_msa.fits'}
2022-12-04 02:37:45,739 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2022-12-04 02:37:45,754 - stpipe.AssignWcsStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:37:45,754 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2022-12-04 02:37:45,764 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2022-12-04 02:37:45,916 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:45,917 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-04 02:37:45,934 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2022-12-04 02:37:45,936 - stpipe.JwstStep - INFO - JwstStep instance created.
2022-12-04 02:37:46,089 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-04 02:37:46,090 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-04 02:37:46,091 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-04 02:37:46,092 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2022-12-04 02:37:46,107 - stpipe.MSAFlagOpenStep - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2022-12-04 02:37:46,263 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2022-12-04 02:37:46,303 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2022-12-04 02:37:46,327 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2022-12-04 02:37:46,403 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2022-12-04 02:37:46,428 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2324.820049828629.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2244.599990785436.
  warnings.warn(f"Invalid interval: upper bound {upper} "
2022-12-04 02:37:58,707 - stpipe.MSAFlagOpenStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:37:58,708 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2022-12-04 02:37:58,721 - stpipe.Extract2dStep - INFO - Extract2dStep instance created.
2022-12-04 02:37:59,025 - stpipe.Extract2dStep - INFO - Step Extract2dStep running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:37:59,026 - stpipe.Extract2dStep - INFO - Step Extract2dStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}
2022-12-04 02:37:59,045 - stpipe.Extract2dStep - INFO - EXP_TYPE is NRS_MSASPEC
2022-12-04 02:37:59,530 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 53
2022-12-04 02:37:59,531 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1542 2048
2022-12-04 02:37:59,532 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1316 1326
2022-12-04 02:37:59,731 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:37:59,741 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2022-12-04 02:37:59,742 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2022-12-04 02:38:00,383 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 54
2022-12-04 02:38:00,384 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1542 2048
2022-12-04 02:38:00,385 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1306 1316
2022-12-04 02:38:00,582 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:00,592 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2022-12-04 02:38:00,593 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2022-12-04 02:38:01,256 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 42
2022-12-04 02:38:01,257 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 2018 2048
2022-12-04 02:38:01,258 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 546 555
2022-12-04 02:38:01,456 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:01,466 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2022-12-04 02:38:01,467 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2022-12-04 02:38:02,148 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 43
2022-12-04 02:38:02,149 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1970 2048
2022-12-04 02:38:02,150 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 415 424
2022-12-04 02:38:02,357 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:02,366 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2022-12-04 02:38:02,367 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2022-12-04 02:38:02,836 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 44
2022-12-04 02:38:02,838 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1969 2048
2022-12-04 02:38:02,838 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 405 414
2022-12-04 02:38:03,033 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:03,043 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2022-12-04 02:38:03,045 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2022-12-04 02:38:03,739 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 45
2022-12-04 02:38:03,741 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1908 2048
2022-12-04 02:38:03,741 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 531 541
2022-12-04 02:38:03,936 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:03,948 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2022-12-04 02:38:03,950 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2022-12-04 02:38:04,639 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 46
2022-12-04 02:38:04,640 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1882 2048
2022-12-04 02:38:04,640 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 203 213
2022-12-04 02:38:04,834 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:04,843 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2022-12-04 02:38:04,845 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2022-12-04 02:38:05,325 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 47
2022-12-04 02:38:05,326 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1815 2048
2022-12-04 02:38:05,327 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 567 576
2022-12-04 02:38:05,524 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:05,535 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2022-12-04 02:38:05,537 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2022-12-04 02:38:06,263 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 48
2022-12-04 02:38:06,264 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1815 2048
2022-12-04 02:38:06,265 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 562 571
2022-12-04 02:38:06,464 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:06,474 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2022-12-04 02:38:06,475 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2022-12-04 02:38:07,188 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 49
2022-12-04 02:38:07,189 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1791 2048
2022-12-04 02:38:07,189 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 632 642
2022-12-04 02:38:07,384 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:07,394 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2022-12-04 02:38:07,395 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2022-12-04 02:38:07,874 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 50
2022-12-04 02:38:07,875 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1774 2048
2022-12-04 02:38:07,875 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 239 249
2022-12-04 02:38:08,075 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:08,085 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2022-12-04 02:38:08,086 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2022-12-04 02:38:08,818 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 51
2022-12-04 02:38:08,819 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1759 2048
2022-12-04 02:38:08,820 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 431 441
2022-12-04 02:38:09,020 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:09,029 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2022-12-04 02:38:09,030 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2022-12-04 02:38:09,505 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 52
2022-12-04 02:38:09,506 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1722 2048
2022-12-04 02:38:09,506 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 804 814
2022-12-04 02:38:09,700 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:09,709 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2022-12-04 02:38:09,711 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2022-12-04 02:38:10,461 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 55
2022-12-04 02:38:10,462 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 1022 2048
2022-12-04 02:38:10,463 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1416 1430
2022-12-04 02:38:10,662 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:10,672 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2022-12-04 02:38:10,673 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2022-12-04 02:38:11,428 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 65
2022-12-04 02:38:11,429 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 427 1893
2022-12-04 02:38:11,429 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1252 1273
2022-12-04 02:38:11,649 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:11,659 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2022-12-04 02:38:11,660 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2022-12-04 02:38:12,145 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 66
2022-12-04 02:38:12,146 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 426 1892
2022-12-04 02:38:12,147 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1453 1474
2022-12-04 02:38:12,361 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:12,370 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2022-12-04 02:38:12,372 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2022-12-04 02:38:13,152 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 68
2022-12-04 02:38:13,153 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 375 1842
2022-12-04 02:38:13,153 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 1477 1500
2022-12-04 02:38:13,370 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:13,380 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2022-12-04 02:38:13,381 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2022-12-04 02:38:13,864 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 56
2022-12-04 02:38:13,865 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 872 2048
2022-12-04 02:38:13,865 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 769 783
2022-12-04 02:38:14,062 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:14,071 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2022-12-04 02:38:14,073 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2022-12-04 02:38:14,834 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 57
2022-12-04 02:38:14,834 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 805 2048
2022-12-04 02:38:14,835 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 355 370
2022-12-04 02:38:15,045 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:15,054 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2022-12-04 02:38:15,056 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2022-12-04 02:38:15,513 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 58
2022-12-04 02:38:15,514 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 731 2048
2022-12-04 02:38:15,514 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 259 275
2022-12-04 02:38:16,045 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:16,055 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2022-12-04 02:38:16,057 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2022-12-04 02:38:16,537 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 59
2022-12-04 02:38:16,538 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 658 2048
2022-12-04 02:38:16,538 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 72 88
2022-12-04 02:38:16,743 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:16,753 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2022-12-04 02:38:16,754 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2022-12-04 02:38:17,536 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 60
2022-12-04 02:38:17,536 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 641 2048
2022-12-04 02:38:17,537 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 682 699
2022-12-04 02:38:17,747 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:17,756 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2022-12-04 02:38:17,758 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2022-12-04 02:38:18,233 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 61
2022-12-04 02:38:18,234 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 620 2048
2022-12-04 02:38:18,234 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 823 840
2022-12-04 02:38:18,443 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:18,452 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2022-12-04 02:38:18,453 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2022-12-04 02:38:19,288 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 62
2022-12-04 02:38:19,289 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 570 2032
2022-12-04 02:38:19,289 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 510 528
2022-12-04 02:38:19,495 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:19,505 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2022-12-04 02:38:19,507 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2022-12-04 02:38:19,989 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 63
2022-12-04 02:38:19,990 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 454 1915
2022-12-04 02:38:19,991 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 182 200
2022-12-04 02:38:20,249 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:20,258 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2022-12-04 02:38:20,259 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2022-12-04 02:38:20,727 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 64
2022-12-04 02:38:20,728 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 454 1915
2022-12-04 02:38:20,729 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 177 195
2022-12-04 02:38:21,279 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:21,288 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2022-12-04 02:38:21,290 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2022-12-04 02:38:21,767 - stpipe.Extract2dStep - INFO - Name of subarray extracted: 67
2022-12-04 02:38:21,768 - stpipe.Extract2dStep - INFO - Subarray x-extents are: 328 1789
2022-12-04 02:38:21,769 - stpipe.Extract2dStep - INFO - Subarray y-extents are: 131 150
2022-12-04 02:38:22,011 - stpipe.Extract2dStep - INFO - set slit_attributes completed
2022-12-04 02:38:22,021 - stpipe.Extract2dStep - INFO - Update S_REGION to POLYGON ICRS  156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2022-12-04 02:38:22,022 - stpipe.Extract2dStep - INFO - Updated S_REGION to POLYGON ICRS  156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2022-12-04 02:38:23,804 - stpipe.Extract2dStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:38:23,805 - stpipe.Extract2dStep - INFO - Step Extract2dStep done
2022-12-04 02:38:26,671 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2022-12-04 02:38:27,020 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:38:27,022 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}
2022-12-04 02:38:27,030 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_MSASPEC
2022-12-04 02:38:27,031 - stpipe.SourceTypeStep - INFO - source_id=53, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,033 - stpipe.SourceTypeStep - INFO - source_id=54, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,034 - stpipe.SourceTypeStep - INFO - source_id=42, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,035 - stpipe.SourceTypeStep - INFO - source_id=43, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,036 - stpipe.SourceTypeStep - INFO - source_id=44, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,038 - stpipe.SourceTypeStep - INFO - source_id=45, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,039 - stpipe.SourceTypeStep - INFO - source_id=46, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,040 - stpipe.SourceTypeStep - INFO - source_id=47, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,042 - stpipe.SourceTypeStep - INFO - source_id=48, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,043 - stpipe.SourceTypeStep - INFO - source_id=49, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,044 - stpipe.SourceTypeStep - INFO - source_id=50, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,046 - stpipe.SourceTypeStep - INFO - source_id=51, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,047 - stpipe.SourceTypeStep - INFO - source_id=52, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,048 - stpipe.SourceTypeStep - INFO - source_id=55, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,049 - stpipe.SourceTypeStep - INFO - source_id=65, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,050 - stpipe.SourceTypeStep - INFO - source_id=66, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,052 - stpipe.SourceTypeStep - INFO - source_id=68, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,053 - stpipe.SourceTypeStep - INFO - source_id=56, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,054 - stpipe.SourceTypeStep - INFO - source_id=57, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,055 - stpipe.SourceTypeStep - INFO - source_id=58, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,056 - stpipe.SourceTypeStep - INFO - source_id=59, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,057 - stpipe.SourceTypeStep - INFO - source_id=60, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,059 - stpipe.SourceTypeStep - INFO - source_id=61, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,060 - stpipe.SourceTypeStep - INFO - source_id=62, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,062 - stpipe.SourceTypeStep - INFO - source_id=63, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,063 - stpipe.SourceTypeStep - INFO - source_id=64, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,064 - stpipe.SourceTypeStep - INFO - source_id=67, stellarity=0.0000, type=EXTENDED
2022-12-04 02:38:27,067 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2022-12-04 02:38:27,136 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2022-12-04 02:38:27,437 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:38:27,438 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-04 02:38:27,503 - stpipe.WavecorrStep - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0004.asdf
2022-12-04 02:38:32,676 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 53
2022-12-04 02:38:32,677 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 54
2022-12-04 02:38:32,677 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 42
2022-12-04 02:38:32,677 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 43
2022-12-04 02:38:32,678 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 44
2022-12-04 02:38:32,678 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 45
2022-12-04 02:38:32,678 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 46
2022-12-04 02:38:32,679 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 47
2022-12-04 02:38:32,679 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 48
2022-12-04 02:38:32,679 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 49
2022-12-04 02:38:32,680 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 50
2022-12-04 02:38:32,681 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 51
2022-12-04 02:38:32,681 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 52
2022-12-04 02:38:32,682 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 55
2022-12-04 02:38:32,682 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 65
2022-12-04 02:38:32,682 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 66
2022-12-04 02:38:32,683 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 68
2022-12-04 02:38:32,683 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 56
2022-12-04 02:38:32,684 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 57
2022-12-04 02:38:32,684 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 58
2022-12-04 02:38:32,684 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 59
2022-12-04 02:38:32,685 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 60
2022-12-04 02:38:32,685 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 61
2022-12-04 02:38:32,686 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 62
2022-12-04 02:38:32,686 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 63
2022-12-04 02:38:32,686 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 64
2022-12-04 02:38:32,687 - stpipe.WavecorrStep - INFO - Detected a EXTENDED source type in slit 67
2022-12-04 02:38:32,691 - stpipe.WavecorrStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:38:32,692 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2022-12-04 02:38:32,748 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2022-12-04 02:38:33,343 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:38:33,346 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2022-12-04 02:38:59,735 - stpipe.FlatFieldStep - INFO - Working on slit 53
2022-12-04 02:39:00,573 - stpipe.FlatFieldStep - INFO - Working on slit 54
2022-12-04 02:39:01,394 - stpipe.FlatFieldStep - INFO - Working on slit 42
2022-12-04 02:39:01,595 - stpipe.FlatFieldStep - INFO - Working on slit 43
2022-12-04 02:39:01,855 - stpipe.FlatFieldStep - INFO - Working on slit 44
2022-12-04 02:39:02,119 - stpipe.FlatFieldStep - INFO - Working on slit 45
2022-12-04 02:39:02,457 - stpipe.FlatFieldStep - INFO - Working on slit 46
2022-12-04 02:39:03,300 - stpipe.FlatFieldStep - INFO - Working on slit 47
2022-12-04 02:39:03,761 - stpipe.FlatFieldStep - INFO - Working on slit 48
2022-12-04 02:39:04,235 - stpipe.FlatFieldStep - INFO - Working on slit 49
2022-12-04 02:39:04,756 - stpipe.FlatFieldStep - INFO - Working on slit 50
2022-12-04 02:39:05,291 - stpipe.FlatFieldStep - INFO - Working on slit 51
2022-12-04 02:39:05,838 - stpipe.FlatFieldStep - INFO - Working on slit 52
2022-12-04 02:39:06,437 - stpipe.FlatFieldStep - INFO - Working on slit 55
2022-12-04 02:39:08,017 - stpipe.FlatFieldStep - INFO - Working on slit 65
2022-12-04 02:39:10,274 - stpipe.FlatFieldStep - INFO - Working on slit 66
2022-12-04 02:39:12,515 - stpipe.FlatFieldStep - INFO - Working on slit 68
2022-12-04 02:39:14,787 - stpipe.FlatFieldStep - INFO - Working on slit 56
2022-12-04 02:39:16,624 - stpipe.FlatFieldStep - INFO - Working on slit 57
2022-12-04 02:39:18,485 - stpipe.FlatFieldStep - INFO - Working on slit 58
2022-12-04 02:39:20,446 - stpipe.FlatFieldStep - INFO - Working on slit 59
2022-12-04 02:39:22,492 - stpipe.FlatFieldStep - INFO - Working on slit 60
2022-12-04 02:39:24,626 - stpipe.FlatFieldStep - INFO - Working on slit 61
2022-12-04 02:39:26,729 - stpipe.FlatFieldStep - INFO - Working on slit 62
2022-12-04 02:39:28,877 - stpipe.FlatFieldStep - INFO - Working on slit 63
2022-12-04 02:39:31,014 - stpipe.FlatFieldStep - INFO - Working on slit 64
2022-12-04 02:39:33,256 - stpipe.FlatFieldStep - INFO - Working on slit 67
2022-12-04 02:39:37,269 - stpipe.FlatFieldStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:39:37,270 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2022-12-04 02:39:37,326 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2022-12-04 02:39:37,789 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-04 02:39:37,791 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-12-04 02:39:37,854 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0002.fits
2022-12-04 02:39:37,923 - stpipe.PathLossStep - INFO - Input exposure type is NRS_MSASPEC
2022-12-04 02:39:43,506 - stpipe.PathLossStep - INFO - Working on slit 0
2022-12-04 02:39:43,528 - stpipe.PathLossStep - INFO - Working on slit 1
2022-12-04 02:39:43,550 - stpipe.PathLossStep - INFO - Working on slit 2
2022-12-04 02:39:43,571 - stpipe.PathLossStep - INFO - Working on slit 3
2022-12-04 02:39:43,591 - stpipe.PathLossStep - INFO - Working on slit 4
2022-12-04 02:39:43,614 - stpipe.PathLossStep - INFO - Working on slit 5
2022-12-04 02:39:43,635 - stpipe.PathLossStep - INFO - Working on slit 6
2022-12-04 02:39:43,656 - stpipe.PathLossStep - INFO - Working on slit 7
2022-12-04 02:39:43,678 - stpipe.PathLossStep - INFO - Working on slit 8
2022-12-04 02:39:43,699 - stpipe.PathLossStep - INFO - Working on slit 9
2022-12-04 02:39:43,720 - stpipe.PathLossStep - INFO - Working on slit 10
2022-12-04 02:39:43,742 - stpipe.PathLossStep - INFO - Working on slit 11
2022-12-04 02:39:43,762 - stpipe.PathLossStep - INFO - Working on slit 12
2022-12-04 02:39:43,784 - stpipe.PathLossStep - INFO - Working on slit 13
2022-12-04 02:39:43,807 - stpipe.PathLossStep - INFO - Working on slit 14
2022-12-04 02:39:43,830 - stpipe.PathLossStep - INFO - Working on slit 15
2022-12-04 02:39:43,853 - stpipe.PathLossStep - INFO - Working on slit 16
2022-12-04 02:39:43,877 - stpipe.PathLossStep - INFO - Working on slit 17
2022-12-04 02:39:43,900 - stpipe.PathLossStep - INFO - Working on slit 18
2022-12-04 02:39:43,924 - stpipe.PathLossStep - INFO - Working on slit 19
2022-12-04 02:39:43,948 - stpipe.PathLossStep - INFO - Working on slit 20
2022-12-04 02:39:43,971 - stpipe.PathLossStep - INFO - Working on slit 21
2022-12-04 02:39:43,994 - stpipe.PathLossStep - INFO - Working on slit 22
2022-12-04 02:39:44,020 - stpipe.PathLossStep - INFO - Working on slit 23
2022-12-04 02:39:44,043 - stpipe.PathLossStep - INFO - Working on slit 24
2022-12-04 02:39:44,066 - stpipe.PathLossStep - INFO - Working on slit 25
2022-12-04 02:39:44,091 - stpipe.PathLossStep - INFO - Working on slit 26
2022-12-04 02:39:44,119 - stpipe.PathLossStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 02:39:44,120 - stpipe.PathLossStep - INFO - Step PathLossStep done
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_mos.py:321: MatplotlibDeprecationWarning: Auto-removal of overlapping axes is deprecated since 3.6 and will be removed two minor releases later; explicitly call ax.remove() as needed.
  plt.subplot(221)

Running test for MOS...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel  -->     Detector: NRS1   Grating: G140M   Filter: F100LP   Lamp: LINE1   EXP_TYPE: NRS_MSASPEC
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0002.fits
 Looping through the slits... 
   Retrieving reference file extensions
Working with slitlet  53
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...

Calculating statistics... 

   Absolute Difference  :   mean = 3.003e-08    median = 3.057e-08    stdev = 3.503e-08
    Maximum   AbsoluteDifference = 1.019e-07
    Minimum   AbsoluteDifference = -4.432e-08
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

* TEST result: corrections residuals median = 3.0027843072897874e-08 threshold difference =  9.999e-05 

 *** Result of the test: PASSED

Working with slitlet  54
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...

Calculating statistics... 

   Absolute Difference  :   mean = 3.022e-08    median = 2.975e-08    stdev = 3.520e-08
    Maximum   AbsoluteDifference = 1.023e-07
    Minimum   AbsoluteDifference = -4.223e-08
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

* TEST result: corrections residuals median = 3.022224755483523e-08 threshold difference =  9.999e-05 

 *** Result of the test: PASSED

Working with slitlet  42
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...

Calculating statistics... 

   Absolute Difference  :   mean = 2.004e-08    median = 1.866e-08    stdev = 3.421e-08
    Maximum   AbsoluteDifference = 8.544e-08
    Minimum   AbsoluteDifference = -4.042e-08
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

* TEST result: corrections residuals median = 2.004418435674893e-08 threshold difference =  9.999e-05 

 *** Result of the test: PASSED

Working with slitlet  43
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...

Calculating statistics... 

   Absolute Difference  :   mean = 2.079e-08    median = 2.087e-08    stdev = 3.468e-08
    Maximum   AbsoluteDifference = 8.930e-08
    Minimum   AbsoluteDifference = -4.479e-08
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

* TEST result: corrections residuals median = 2.078751090862669e-08 threshold difference =  9.999e-05 

 *** Result of the test: PASSED

Working with slitlet  44
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...

Calculating statistics... 

   Absolute Difference  :   mean = 2.225e-08    median = 2.276e-08    stdev = 3.474e-08
    Maximum   AbsoluteDifference = 8.536e-08
    Minimum   AbsoluteDifference = -4.266e-08
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

* TEST result: corrections residuals median = 2.2254868009763256e-08 threshold difference =  9.999e-05 

 *** Result of the test: PASSED

Working with slitlet  45
   Slitlet name in input file and in pathloss output file are the same.
   Retrieved extended/uniform source extension 3
   slit_x, slit_y (-0.5, -0.5)
   Running test for UNIFORM source...


# Quickly see if the test passed 

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<42} {:<8}'.format(key, val))

These are the final results of the tests: 
mos_g140m_line1_NRS1_uncal.fits            All slits PASSED path_loss test.
mos_g140m_line1_NRS2_uncal.fits            All slits PASSED path_loss test.

/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/sre_parse.py:501: ResourceWarning: unclosed file <_io.BufferedReader name='/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/.astropy/cache/download/url/8e6d6917d5834a76434dc30e12182a4d/contents'>
  sourcematch = source.match

JWST Pipeline Validation Testing Notebook: spec2, pathloss step for mos¶

Table of Contents¶

Imports¶

Test Description¶

Results¶

Calibration WG Requested Algorithm:¶

Defining Term¶

Run the JWST pipeline and pathloss validation tests¶

Testing Data Set¶

About this Notebook¶